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  2. Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of v...

    Authors: Késia Silva Lourenço, Afnan K. A. Suleiman, A. Pijl, J. A. van Veen, H. Cantarella and E. E. Kuramae
    Citation: Microbiome 2018 6:142
    Content type: Research Published on:

  3. Pathogen colonization inside tick tissues is a significant aspect of the overall competence of a vector. Amblyomma maculatum is a competent vector of the spotted fever group rickettsiae, Rickettsia parkeri. When

    Authors: Khemraj Budachetri, Deepak Kumar, Gary Crispell, Christine Beck, Gregory Dasch and Shahid Karim
    Citation: Microbiome 2018 6:141
    Content type: Research Published on:

  5. Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), has led to the deaths of millions of hibernating bats in the United States of America (USA) and Canada. Efficient strate...

    Authors: Amanpreet Singh, Erica Lasek-Nesselquist, Vishnu Chaturvedi and Sudha Chaturvedi
    Citation: Microbiome 2018 6:139
    Content type: Research Published on:

  6. Microorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetl...

    Authors: Paula Dalcin Martins, Robert E. Danczak, Simon Roux, Jeroen Frank, Mikayla A. Borton, Richard A. Wolfe, Marie N. Burris and Michael J. Wilkins
    Citation: Microbiome 2018 6:138
    Content type: Research Published on:

  7. Dysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set o...

    Authors: Emmanuel Montassier, Gabriel A. Al-Ghalith, Benjamin Hillmann, Kimberly Viskocil, Amanda J. Kabage, Christopher E. McKinlay, Michael J. Sadowsky, Alexander Khoruts and Dan Knights
    Citation: Microbiome 2018 6:137
    Content type: Methodology Published on:

  8. Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied ...

    Authors: Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Siyuan Liang, Yang Chen, Haisong Lin, Xiujuan Zhu, Shengzhu Huang, Jiarong Tian…
    Citation: Microbiome 2018 6:136
    Content type: Research Published on:

  9. Behcet’s disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but...

    Authors: Zi Ye, Ni Zhang, Chunyan Wu, Xinyuan Zhang, Qingfeng Wang, Xinyue Huang, Liping Du, Qingfeng Cao, Jihong Tang, Chunjiang Zhou, Shengping Hou, Yue He, Qian Xu, Xiao Xiong, Aize Kijlstra, Nan Qin…
    Citation: Microbiome 2018 6:135
    Content type: Research Published on:

  10. As the gut microbiota contributes to metabolic health, it is important to determine specific diet-microbiota interactions that influence host metabolism. Bile acids and dietary fat source can alter phenotypes ...

    Authors: Sarah Just, Stanislas Mondot, Josef Ecker, Katrin Wegner, Eva Rath, Laura Gau, Theresa Streidl, Genevieve Hery-Arnaud, Sinah Schmidt, Till Robin Lesker, Valentin Bieth, Andreas Dunkel, Till Strowig, Thomas Hofmann, Dirk Haller, Gerhard Liebisch…
    Citation: Microbiome 2018 6:134
    Content type: Research Published on:

  11. Different dietary approaches, such as gluten and casein free diets, or the use of probiotics and prebiotics have been suggested in autistic spectrum disorders in order to reduce gastrointestinal (GI) disturban...

    Authors: Roberta Grimaldi, Glenn R. Gibson, Jelena Vulevic, Natasa Giallourou, Josué L. Castro-Mejía, Lars H. Hansen, E. Leigh Gibson, Dennis S. Nielsen and Adele Costabile
    Citation: Microbiome 2018 6:133
    Content type: Research Published on:

  14. Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distr...

    Authors: An Ni Zhang, Li-Guan Li, Liping Ma, Michael R. Gillings, James M. Tiedje and Tong Zhang
    Citation: Microbiome 2018 6:130
    Content type: Research Published on:

  16. The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location i...

    Authors: Jose M. Haro-Moreno, Mario López-Pérez, José R. de la Torre, Antonio Picazo, Antonio Camacho and Francisco Rodriguez-Valera
    Citation: Microbiome 2018 6:128
    Content type: Research Published on:

  17. Unfortunately, after publication of this article [1], it was noticed that the accession numbers for the study were missing. The correct numbers are PRJNA438554, SRP148953.

    Authors: Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R. Gillings, Hong Chen, Tong Zhang and Yong-Guan Zhu
    Citation: Microbiome 2018 6:127
    Content type: Correction Published on:

    The original article was published in Microbiome 2017 5:84

  18. Following publication of the original article [1], the authors reported an error in the caption of Fig. 4.

    Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang
    Citation: Microbiome 2018 6:126
    Content type: Correction Published on:

    The original article was published in Microbiome 2018 6:103

  20. Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining ...

    Authors: Donald D. Nyangahu, Katie S. Lennard, Bryan P. Brown, Matthew G. Darby, Jerome M. Wendoh, Enock Havyarimana, Peter Smith, James Butcher, Alain Stintzi, Nicola Mulder, William Horsnell and Heather B. Jaspan
    Citation: Microbiome 2018 6:124
    Content type: Research Published on:

  21. Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on...

    Authors: Masood ur Rehman Kayani, Shawn M. Doyle, Naseer Sangwan, Guanqun Wang, Jack A. Gilbert, Brent C. Christner and Ting F. Zhu
    Citation: Microbiome 2018 6:123
    Content type: Microbiome Announcement Published on:

  22. The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of ...

    Authors: Sara N. Lundgren, Juliette C. Madan, Jennifer A. Emond, Hilary G. Morrison, Brock C. Christensen, Margaret R. Karagas and Anne G. Hoen
    Citation: Microbiome 2018 6:109
    Content type: Research Published on:

  23. The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowl...

    Authors: Evan P. Starr, Shengjing Shi, Steven J. Blazewicz, Alexander J. Probst, Donald J. Herman, Mary K. Firestone and Jillian F. Banfield
    Citation: Microbiome 2018 6:122
    Content type: Research Published on:

  24. One way to improve both the ecological performance and functionality of probiotic bacteria is by combining them with a prebiotic in the form of a synbiotic. However, the degree to which such synbiotic formulat...

    Authors: Janina A. Krumbeck, Heather E. Rasmussen, Robert W. Hutkins, Jennifer Clarke, Krista Shawron, Ali Keshavarzian and Jens Walter
    Citation: Microbiome 2018 6:121
    Content type: Research Published on:

  25. Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and communi...

    Authors: Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D. Washburne, Didier Gonze and Stefanie Widder
    Citation: Microbiome 2018 6:120
    Content type: Research Published on:

  26. Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology ...

    Authors: Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez and Alberto López-Bueno
    Citation: Microbiome 2018 6:119
    Content type: Methodology Published on:

  27. Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are cruc...

    Authors: Muhammad Farhan Ul Haque, Andrew T. Crombie, Scott A. Ensminger, Calin Baciu and J. Colin Murrell
    Citation: Microbiome 2018 6:118
    Content type: Research Published on:

  29. Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this ...

    Authors: Hirokazu Toju, Akifumi S. Tanabe and Hirotoshi Sato
    Citation: Microbiome 2018 6:116
    Content type: Research Published on:

  30. The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of ...

    Authors: Ramesh J. Pandit, Ankit T. Hinsu, Namrata V. Patel, Prakash G. Koringa, Subhash J. Jakhesara, Jalpa R. Thakkar, Tejas M. Shah, Georgina Limon, Androniki Psifidi, Javier Guitian, David A. Hume, Fiona M. Tomley, Dharamshibhai N. Rank, M. Raman, K. G. Tirumurugaan, Damer P. Blake…
    Citation: Microbiome 2018 6:115
    Content type: Research Published on:

  31. Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding...

    Authors: Marie-Lara Bouffaud, Sébastien Renoud, Audrey Dubost, Yvan Moënne-Loccoz and Daniel Muller
    Citation: Microbiome 2018 6:114
    Content type: Research Published on:

  32. The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be...

    Authors: Bernhard Tschitschko, Susanne Erdmann, Matthew Z. DeMaere, Simon Roux, Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sarah Brazendale, Alyce M. Hancock, Emiley A. Eloe-Fadrosh and Ricardo Cavicchioli
    Citation: Microbiome 2018 6:113
    Content type: Research Published on:

  33. The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it ...

    Authors: Brandon Brooks, Matthew R. Olm, Brian A. Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina R. Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz and Jillian F. Banfield
    Citation: Microbiome 2018 6:112
    Content type: Research Published on:

  34. Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding form...

    Authors: Lee Call, Barbara Stoll, Berthe Oosterloo, Nadim Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian Berg, Joseph Petrosino, Oluyinka Olutoye and Douglas Burrin
    Citation: Microbiome 2018 6:111
    Content type: Research Published on:

  36. In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polari...

    Authors: Kirk E. Anderson, Vincent A. Ricigliano, Brendon M. Mott, Duan C. Copeland, Amy S. Floyd and Patrick Maes
    Citation: Microbiome 2018 6:108
    Content type: Research Published on:

  37. The gut microbiota is closely associated with gastrointestinal (GI) motility disorder, but the mechanism(s) by which bacteria interact with and affect host GI motility remains unclear. In this study, through u...

    Authors: Ling Zhao, Yufen Huang, Lin Lu, Wei Yang, Tao Huang, Zesi Lin, Chengyuan Lin, Hiuyee Kwan, Hoi Leong Xavier Wong, Yang Chen, Silong Sun, Xuefeng Xie, Xiaodong Fang, Huanming Yang, Jian Wang, Lixin Zhu…
    Citation: Microbiome 2018 6:107
    Content type: Research Published on:

  38. pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe,...

    Authors: Daniel R. Lammel, Gabriel Barth, Otso Ovaskainen, Leonardo M. Cruz, Josileia A. Zanatta, Masahiro Ryo, Emanuel M. de Souza and Fábio O. Pedrosa
    Citation: Microbiome 2018 6:106
    Content type: Research Published on:

  39. Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the seque...

    Authors: Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Eric Pelletier, Ian Probert, Johan Decelle, Stéphane Le Crom, Fabrice Not and Lucie Bittner
    Citation: Microbiome 2018 6:105
    Content type: Research Published on:

  40. Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will r...

    Authors: Juliana Durack, Yvonne J. Huang, Snehal Nariya, Laura S. Christian, K. Mark Ansel, Avraham Beigelman, Mario Castro, Anne-Marie Dyer, Elliot Israel, Monica Kraft, Richard J. Martin, David T. Mauger, Sharon R. Rosenberg, Tonya S. King, Steven R. White, Loren C. Denlinger…
    Citation: Microbiome 2018 6:104
    Content type: Research Published on:

  41. Huddling is highly evolved as a cooperative behavioral strategy for social mammals to maximize their fitness in harsh environments. Huddling behavior can change psychological and physiological responses. The c...

    Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang
    Citation: Microbiome 2018 6:103
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2018 6:126

  42. As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.

    Authors: Xiaobo Liu, Meng Li, Cindy J. Castelle, Alexander J. Probst, Zhichao Zhou, Jie Pan, Yang Liu, Jillian F. Banfield and Ji-Dong Gu
    Citation: Microbiome 2018 6:102
    Content type: Research Published on:

  43. In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces un...

    Authors: Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves…
    Citation: Microbiome 2018 6:101
    Content type: Microbiome Announcement Published on:

  44. Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the P...

    Authors: Jacqueline R. Starr, Yanmei Huang, Kyu Ha Lee, C. M. Murphy, Anna-Barbara Moscicki, Caroline H. Shiboski, Mark I. Ryder, Tzy-Jyun Yao, Lina L. Faller, Russell B. Van Dyke and Bruce J. Paster
    Citation: Microbiome 2018 6:100
    Content type: Research Published on:

  47. Variation in induced models of autoimmunity has been attributed to the housing environment and its effect on the gut microbiota. In Graves’ disease (GD), autoantibodies to the thyrotropin receptor (TSHR) cause...

    Authors: Giulia Masetti, Sajad Moshkelgosha, Hedda-Luise Köhling, Danila Covelli, Jasvinder Paul Banga, Utta Berchner-Pfannschmidt, Mareike Horstmann, Salvador Diaz-Cano, Gina-Eva Goertz, Sue Plummer, Anja Eckstein, Marian Ludgate, Filippo Biscarini and Julian Roberto Marchesi
    Citation: Microbiome 2018 6:97
    Content type: Research Published on:

  49. The early-life gut microbiota plays a critical role in host metabolism in later life. However, little is known about how the fatty acid profile of the maternal diet during gestation and lactation influences th...

    Authors: Ruairi C. Robertson, Kanakaraju Kaliannan, Conall R. Strain, R. Paul Ross, Catherine Stanton and Jing X. Kang
    Citation: Microbiome 2018 6:95
    Content type: Research Published on:

  50. After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in de...

    Authors: Melhem Bilen, Jean-Charles Dufour, Jean-Christophe Lagier, Fréderic Cadoret, Ziad Daoud, Grégory Dubourg and Didier Raoult
    Citation: Microbiome 2018 6:94
    Content type: Review Published on:
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